Mercurial > repos > jjohnson > gatk2
comparison variant_combine.xml @ 35:a29c7d7d962d draft
Fix default read filter screening
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 01 Mar 2013 07:52:02 -0600 |
| parents | b99c25b0ad4d |
| children | 14d47237bb0a |
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| 34:b99c25b0ad4d | 35:a29c7d7d962d |
|---|---|
| 37 #end for | 37 #end for |
| 38 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: | 38 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: |
| 39 -p '--pedigreeString "${pedigree_string.pedigree_string}"' | 39 -p '--pedigreeString "${pedigree_string.pedigree_string}"' |
| 40 #end for | 40 #end for |
| 41 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' | 41 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' |
| 42 #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] | 42 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] |
| 43 #for $read_filter in $gatk_param_type.read_filter: | 43 #for $read_filter in $gatk_param_type.read_filter: |
| 44 -p ' | 44 -p ' |
| 45 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: | 45 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters: |
| 46 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" | 46 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" |
| 47 #end_if | 47 #end_if |
| 48 #for $name, $param in $read_filter.read_filter_type.iteritems(): | 48 #for $name, $param in $read_filter.read_filter_type.iteritems(): |
| 49 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: | 49 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: |
| 50 #if hasattr( $param.input, 'truevalue' ): | 50 #if hasattr( $param.input, 'truevalue' ): |
| 210 </when> | 210 </when> |
| 211 <when value="FailsVendorQualityCheck"> | 211 <when value="FailsVendorQualityCheck"> |
| 212 <!-- no extra options --> | 212 <!-- no extra options --> |
| 213 </when> | 213 </when> |
| 214 <when value="MalformedRead"> | 214 <when value="MalformedRead"> |
| 215 <!-- no extra options --> | 215 <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> |
| 216 </when> | 216 </when> |
| 217 <when value="MappingQuality"> | 217 <when value="MappingQuality"> |
| 218 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> | 218 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> |
| 219 </when> | 219 </when> |
| 220 <when value="MappingQualityUnavailable"> | 220 <when value="MappingQualityUnavailable"> |